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Technical considerations for functional sequencing assays

Nature Immunology volume 13, pages 802–807 (2012)Cite this article

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Abstract

Next-generation sequencing technologies need careful design of experiments and evaluation of results to meet field requirements. Here we discuss technical considerations for these high-throughput assays, together with criteria to assess the quality of the results and the necessary validation.

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Figure 1: RNA-seq work flow.
Figure 2: DNase-seq work flow.
Figure 3: Hi-C and ChIA-PET work flow.

References

  1. Kidder, B.L., Hu, G. & Zhao, K. Nat. Immunol. 12, 918–922 (2011).

    Article  CAS  Google Scholar 

  2. Mortazavi, A., Williams, B.A., Mccue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).

    Article  CAS  Google Scholar 

  3. Cloonan, N. et al. Nat. Methods 5, 613–619 (2008).

    Article  CAS  Google Scholar 

  4. Hesselberth, J.R. et al. Nat. Methods 6, 283–289 (2009).

    Article  CAS  Google Scholar 

  5. Boyle, A.P. et al. Genome Res. 21, 456–464 (2011).

    Article  CAS  Google Scholar 

  6. Dostie, J. & Dekker, J. Nat. Protoc. 2, 988–1002 (2007).

    Article  CAS  Google Scholar 

  7. Fullwood, M.J. et al. Nature 462, 58–64 (2009).

    Article  CAS  Google Scholar 

  8. Trapnell, C. et al. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  Google Scholar 

  9. Linsen, S.E.V. et al. Nat. Methods 6, 474–476 (2009).

    Article  CAS  Google Scholar 

  10. Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011).

    Article  CAS  Google Scholar 

  11. Robertson, G. et al. Nat. Methods 7, 909–912 (2010).

    Article  CAS  Google Scholar 

  12. Bahn, J.H. et al. Genome Res. 22, 142–150 (2012).

    Article  CAS  Google Scholar 

  13. Schroeder, A. et al. BMC Mol. Biol. 7, 3 (2006).

    Article  Google Scholar 

  14. Tang, F. et al. Nat. Protoc. 5, 516–535 (2010).

    Article  CAS  Google Scholar 

  15. Cui, P. et al. Genomics 96, 259–265 (2010).

    Article  CAS  Google Scholar 

  16. Parkhomchuk, D. et al. Nucleic Acids Res. 37, e123 (2009).

    Article  Google Scholar 

  17. Lister, R. et al. Cell 133, 523–536 (2008).

    Article  CAS  Google Scholar 

  18. Gertz, J. et al. Genome Res. 22, 134–141 (2012).

    Article  CAS  Google Scholar 

  19. Trapnell, C. et al. Nat. Protoc. 7, 562–578 (2012).

    Article  CAS  Google Scholar 

  20. Guttman, M. et al. Nat. Biotechnol. 28, 503–510 (2010).

    Article  CAS  Google Scholar 

  21. Li, B. & Dewey, C.N. BMC Bioinformatics 12, 323 (2011).

    Article  CAS  Google Scholar 

  22. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. Bioinformatics 26, 139–140 (2010).

    Article  CAS  Google Scholar 

  23. Anders, S. & Huber, W. Genome Biol. 11, R106 (2010).

    Article  CAS  Google Scholar 

  24. Wang, L., Feng, Z., Wang, X., Wang, X. & Zhang, X. Bioinformatics 26, 136–138 (2010).

    Article  Google Scholar 

  25. Montgomery, S.B. et al. Nature 464, 773–777 (2010).

    Article  CAS  Google Scholar 

  26. Pickrell, J.K. et al. Nature 464, 768–772 (2010).

    Article  CAS  Google Scholar 

  27. Wang, K., Li, M. & Hakonarson, H. Nucleic Acids Res. 38, e164 (2010).

    Article  Google Scholar 

  28. Gross, D.S. & Garrard, W.T. Annu. Rev. Biochem. 57, 159–197 (1998).

    Article  Google Scholar 

  29. Boyle, A.P., Guinney, J., Crawford, G.E. & Furey, T.S. Bioinformatics 24, 2537–2538 (2008).

    Article  CAS  Google Scholar 

  30. Sabo, P.J. et al. Proc. Natl. Acad. Sci. USA 101, 16837–16842 (2004).

    Article  CAS  Google Scholar 

  31. Hardison, R.C. & Taylor, J. Nat. Rev. Genet. 13, 469–483 (2012).

    Article  CAS  Google Scholar 

  32. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Science 295, 1306–1311 (2002).

    Article  CAS  Google Scholar 

  33. Göndör, A., Rougier, C. & Ohlsson, R. Nat. Protoc. 3, 303–313 (2008).

    Article  Google Scholar 

  34. Lieberman-Aiden, E. et al. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

  35. Dixon, J.R. et al. Nature 485, 376–380 (2012).

    Article  CAS  Google Scholar 

  36. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. & Chen, L. Nat. Biotechnol. 30, 90–98 (2012).

    Article  CAS  Google Scholar 

  37. Yaffe, E. & Tanay, A. Nat. Genet. 43, 1059–1065 (2011).

    Article  CAS  Google Scholar 

  38. Li, G. et al. Genome Biol. 11, R22 (2010).

    Article  Google Scholar 

  39. Dorschner, M.O. et al. Nat. Methods 1, 219–225 (2004).

    Article  CAS  Google Scholar 

  40. Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Nat. Methods 7, 1009–1015 (2010).

    Article  CAS  Google Scholar 

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Acknowledgements

The work of A.M. on this manuscript was supported by the University of California Irvine Center for Complex Biological Systems and US National Institutes of Health P50 GM076516. We thank I. Blitz, S. Sandmeyer, M. Ho, R. Murad, R. Ramirez, M. Macchietto and E. Park for many helpful discussions of this manuscript.

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Authors and Affiliations

  1. Weihua Zeng and Ali Mortazavi are in the Department of Developmental and Cell Biology, University of California, Irvine, California, USA and at the Center for Complex Biological Systems, University of California, Irvine, California, USA.,

    Weihua Zeng & Ali Mortazavi

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  1. Weihua Zeng
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  2. Ali Mortazavi
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Correspondence to Ali Mortazavi.

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The authors declare no competing financial interests.

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Zeng, W., Mortazavi, A. Technical considerations for functional sequencing assays. Nat Immunol 13, 802–807 (2012). https://doi.org/10.1038/ni.2407

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